NexusFile (biojava-legacy 1.9.5 API)

java.lang.Object
- org.biojavax.bio.phylo.io.nexus.NexusFile

```
public class NexusFile
extends Object
```
Represents Nexus files.

Since:

1.6

Author:

Richard Holland, Tobias Thierer, Jim Balhoff

Constructor Summary

Constructors
Constructor Description

NexusFile()

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`addObject(NexusObject object)`	Appends an object to the end of the file.
`Iterator`	`blockIterator()`	Iterate over all blocks in the file in order.
`Iterator`	`commentIterator()`	Iterate over all comments in the file in order.
`boolean`	`containsObject(NexusObject object)`	Checks to see if we contain an object.
`void`	`insertObject(NexusObject object, int pos)`	Inserts an object at the given position.
`Iterator`	`objectIterator()`	Iterate over all objects in the file in order.
`void`	`removeObject(NexusObject object)`	Removes an object from the file.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Constructor Detail
  - NexusFile
```
public NexusFile()
```
- Method Detail
  - addObject
```
public void addObject(NexusObject object)
```
    Appends an object to the end of the file.
    
    Parameters:
    
    object - the NexusObject to append.
  - insertObject
```
public void insertObject(NexusObject object,
                         int pos)
```
    Inserts an object at the given position.
    
    Parameters:
    
    object - the NexusObject to insert.
    
    pos - the position (0-indexed) to add it at.
  - removeObject
```
public void removeObject(NexusObject object)
```
    Removes an object from the file.
    
    Parameters:
    
    object - the NexusObject to remove.
  - containsObject
```
public boolean containsObject(NexusObject object)
```
    Checks to see if we contain an object.
    
    Parameters:
    
    object - the NexusObject to check.
    
    Returns:
    
    true if we contain it.
  - objectIterator
```
public Iterator objectIterator()
```
    Iterate over all objects in the file in order.
    
    Returns:
    
    an iterator of NexusObjects.
  - commentIterator
```
public Iterator commentIterator()
```
    Iterate over all comments in the file in order.
    
    Returns:
    
    an iterator of NexusComments.
  - blockIterator
```
public Iterator blockIterator()
```
    Iterate over all blocks in the file in order.
    
    Returns:
    
    an iterator of NexusBlocks.